Template-catalyzed, disulfide conjugation of monoclonal antibodies

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Template-catalyzed, disulfide conjugation of monoclonal antibodies using a natural amino acid tag. Jeremy D King, Yuelong Ma, Yi-Chui Kuo, Krzysztof P. Bzymek, Leah H Goodstein, Kassondra Meyer, Roger E Moore, Desiree Crow, David Colcher, Gagandeep Singh, David A. Horne, and John C Williams Bioconjugate Chem., Just Accepted Manuscript • DOI: 10.1021/acs.bioconjchem.8b00284 • Publication Date (Web): 15 May 2018 Downloaded from http://pubs.acs.org on May 17, 2018

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Bioconjugate Chemistry

TemplateTemplate-Catalyzed, Disulfide Conjugation of Monoclonal Monoclonal Antibodies Using a Natural Amino Acid Acid Tag. ag. Jeremy D. King1, Yuelong Ma1, Yi-Chui Kuo1, Krzysztof P. Bzymek1, Leah H. Goodstein1, Kassondra Meyer1, Roger Moore2, Desiree Crow2, David M. Colcher2, Gagandeep Singh3, David A. Horne1, and John C. Williams1† Departments of Molecular Medicine1, Molecular Immunology2 and Surgery3 Beckman Research Institute of City of Hope 1500 Duarte Rd, Duarte CA 91010 †

Corresponding author: John C. Williams Email: [email protected]

ABSTRACT: The high specificity and favorable pharmacological properties of monoclonal antibodies (mAbs) have prompted significant interest in re-engineering this class of molecules to add novel functionalities for enhanced therapeutic and diagnostic potential. Here, we used the high affinity, meditope-Fab interaction to template and drive the rapid, efficient, and stable site-specific formation of a disulfide bond. We demonstrate that this template-catalyzed strategy provides a consistent and reproducible means to conjugate fluorescent dyes, cytotoxins, or “click” chemistry handles to meditope-enabled mAbs (memAbs) and memFabs. More importantly, we demonstrate this covalent functionalization is achievable using natural amino acids only, opening up the opportunity to genetically encode cysteine meditope “tags” to biologics. As proof of principle, genetically-encoded, cysteine meditope tags were added to the N- and/or C- termini of fluorescent proteins, nanobodies, and affibodies, each expressed in bacteria, purified to homogeneity and efficiently conjugated to different memAbs and meFabs. We further show that multiple T-cell and Her2-targeting bispecific molecules using this strategy potently activate T-cell signaling pathways in vitro. Finally, the resulting products are highly stable as evidenced by serum stability assays (>14 d at 37 ºC) and in vivo imaging of tumor xenographs. Collectively, the platform offers the opportunity to build and exchange an array of functional moieties, including protein biologics, among any cysteine memAb or Fab to rapidly create, test and optimize stable, multifunctional biologics.

Monoclonal antibodies (mAbs) have long been considered “magic bullets” that seek and destroy diseased cells(1). Due to their specificity and favorable pharmacological properties and positive clinical outcomes, mAbs have become a major therapeutic modality. However, their efficacy is frequently limited, often because of development of resistance to the mAbs and/or suppression of the immune system(2). To exploit the favorable properties of mAbs and circumvent mechanisms of resistance, tremendous efforts have been made, both in academia and industry, to add additional functionality to mAbs. These efforts include conjugation of ultra-potent cytotoxins, fusion of cytokines, and generation of bispecific or multispecific mAbs to produce an artificial immunological synapse. Although each of these approaches has merits, they all invariably require specialized chemistries and/or multiple rounds of optimization, which are labor intensive and must be uniquely developed for each system(3, 4). Herein, we describe a highly stable and facile means to attach small molecules and proteins to mAbs by using the meditope technology. This enables the rapid, efficient exchange of nearly any functionality among

meditope-enabled mAbs and eliminates extensive reengineering efforts. The meditope technology involves the interaction of a cyclic, twelve amino acid peptide and a unique binding site within the Fab arm of cetuximab, which we envisioned could be used as a hitch for attaching drugs and biologics to antibodies(5). The initial affinity of the meditope-Fab interaction was too weak for in vivo use. Through extensive structure-activity relationships, we have significantly improved the affinity of the interaction (KD = 860 pM) and demonstrated that the binding site can be readily grafted onto other mAbs (5-11). More recently, we synthesized and incorporated a non-natural amino acid in the meditope and used click chemistry to create an interlocked mechanical bond to ‘bolt’ meditopes bearing differing functionalities onto the mAb(12). Although the mechanical bond offers a method for stably attaching small-molecules, the use of a non-natural amino acid precludes the direct conjugation of proteins. Here, we introduced a disulfide bond between the meditope peptide and Fab arm to create a stable interaction for antibody

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functionalization using only natural amino acids. We attached an array of proteins and small-molecules to multiple mAbs with this technology. We found that antigen binding is indistinguishable from parental mAbs. Significantly, we found that the disulfide bond stabilizes the Fab, increasing the melting temperature by 10 degrees. The stabilization of the Fab is in sharp contrast to existing methods of functionalization, which typically decreases the stability of the Fab. Ultimately, the platform allows for a single mAb to be rapidly functionalized for drug delivery, tumor imaging, biologic delivery, or immune cell recruitment without the need for additional reengineering.

Scheme 1 – Template-catalyzed, disulfide bond

Results and Discussion Disulfide Introduction Because the interlocked mechanical bond described above requires non-natural amino acids(12), we investigated whether the meditope-Fab interaction could template and catalyze the formation of a disulfide bond using only naturally encoded amino acids (13, 14). To this end, we identified Ser6 on the meditope and Ala175 on the heavy chain of the Fab as candidates for disulfide formation. In the crystal structure of meditopeenabled trastuzumab with meditope (pdb 5U5F), Ser6 and Ala175 are juxtaposed and should be amendable to modification (Scheme 1). We mutated Ala175 in the trastuzumab mAb to cysteine (referred to as 175Cys throughout), and then produced and purified the modified mAb to homogeneity. We also replaced Ser6 of the meditope with cysteine. To avoid the possibility of incorrect disulfide pairings within the cyclic meditope, we replaced the cysteines at positions 1 and 12 with serines, affording the linear meditope SQFDFCTRRLQSGGSK or the higher affinity variant SQFDA(Ph)2CTRRLQSGGSK. We confirmed the formation and specificity of the templatecatalyzed reaction by liquid chromatography mass spectrometry (LCMS). LCMS indicated the cysteine meditope efficiently reacted with the 175Cys-Fab, going to completion within 180 min (Figure 1). Use of Fab/meditope combinations lacking their respective thiols confirmed the specificity of the reaction (Figure S1). The parental Fab (i.e., Ala175) did not react with the high affinity SQFDA(Ph)2CTRRLQSGGSK meditope(12), nor did the 175Cys-Fab when the thiol was blocked using io-

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doacetamide, nor the 175Cys-Fab with the serine meditope variant SQFDA(Ph)2STRRLQSGGSK (Figure S1).

Figure 1. LC/MS was used to follow the formation of the disulfide bond between the 175Cys-Fab and SQFDA(Ph)2CTRRLQSGGSK meditope. A, from top to bottom, LC/MS characterization of the initial sample, sample after 60 min (midpoint), and at reaction completion (180 min), showing a mass shift corresponding to a single meditope (1846 Da). B, reaction completion over time.

Diffraction studies of the templated disulfide bond indicated clear electron density for the meditope peptide and disulfide bond. The bond length and the stereo-chemical values were consistent with a disulfide bond (Figure 2A). A second structure crystallized with an alternative cysteine meditope also indicated formation of a disulfide bond (Figure 2B). No electron density corresponding to a disulfide bond was observed in the apo or serine meditope–175Cys-Fab structures, which served as controls (Figure 2C-D, Table S1). The overall structure of each modified Fab with or without a meditope peptide was unperturbed compared to the parental Fab (RMSD < 0.68 Å, Table S2).


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Figure 2. Electron density maps of the meditope binding site in the 175Cys-Fab with meditope A,B, and D or with meditope C. The light and heavy chains are drawn in light gray, and the meditope is shown in green. The 175Cys thiol is reduced in the apo structure in a. Clear electron density corresponding to a disulfide bond was present when the 175Cys crystals contained the the natural amino acid cysteine meditope as in A or the high affinity diphenylalanine meditope as in B. No electron density for a disulfide was present with the apo structure in C or serine meditope control in D.

In addition, surface plasmon resonance (SPR) revealed no discernible differences in the derived on-rate (ka) or off-rate (kd) among the disulfide conjugated, apo- or parental Fabs to the antigen, consistent with our previous observations(5-7, 912) (Figure 3A, Table S3). The thermal stability of the 175Cys-Fab–SQFDA(Ph)2CTRRLQSGGSK complex was substantially higher (Tm = 81.2 ºC) than that of the 175Cys variant (Tm = 70.9 ºC) or the parental Fab (Tm = 70.8 ºC) (Figure 3B) as shown by differential scanning fluorometry. The 10 ºC increase in thermal stability likely reflects favorable interactions between the meditope and the Fab framework. A large molar excess of the non-modified meditope (50-fold) also produced a similar shift with the parental mAb (Figure S2).

Figure 3. Verifying the activity and stability of the 175Cys Fab before and after conjugation with cysteine meditope. A. Surface plasmon resonance using parental Fab, 175Cys-Fab, and 175CysFab conjugated with SQFDA(Ph)2CTRRLQSGGSK (175Cys conjugate) as analytes and the extracellular domain of HER2 as the ligand fixed to the SPR chip. B. Differential scanning fluorimetry analysis of the parental Fab, 175Cys-Fab, or 175Cys-Fab conjugated SQFDA(Ph)2CTRRLQSGGSK (175Cys conjugate). The 175Cys conjugate shows greater resistance to thermal denaturation. The hash mark indicates the inflection point (e.g., Tm) for each construct.

Conjugating Protein Biologics The efficiency and stabilizing effect of the templated disulfide bond prompted us to proceed with attaching protein biologics to memAbs by using the cysteine meditope peptide sequence as a fusion tag. First, we added the original meditope sequence, SQFDLCTRRLQS, to the N-terminus of the fluorescent protein Eos3.2. Formation of the templated disulfide bond between the bacterially-expressed cys-meditope-Eos3.2 and 175Cys-Fab went to completion within four hours (Figure S3). To avoid self dimerization of Eos3.2, we switched to moxGFP, a monomeric cysteine-free GFP variant(15). The cysmeditope tag was fused on the N-, C- or both termini of mox-



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GFP (Figure 4A). All of these cys-meditope constructs readily reacted with 175Cys-Fab (Figure 4B). SPR measurements indicated that addition of moxGFP did not affect antigen binding (Figure 4C, Figure S4). Thus, these studies indicate that we can attach proteins bearing a cysteine-meditope tag on their N-, C- or both termini to Fabs to create novel antibody conjugates or multivalent Fab conjugates.

Figure 4. Functionalization of Fabs using genetically-encoded moxGFP. A. Diagram of moxGFP (magenta) bearing the cysteine meditope sequence (green with cysteine in orange) at the N-, Ctermini, or both (NC). B. SDS-PAGE (run under non-reducing conditions) showing conjugation of the meditope-GFP variants to 175Cys-Fab. C. SPR studies of the N-, C-, and NC-moxGFP / 175Cys-Fab complexes indicating that the conjugated GFP variants do not reduce antigen binding. Shown are representative traces for each complex at 313 pM. The slightly longer off rate for the NC-moxGFP / Fab complex likely indicates multivalent binding. Complete titrations for each construct are shown in Figure S4.

Another use of mAbs involves bispecific T cell or NK cell engagers, which require complicated assembly that often affects their stability and other critical parameters that influence clinical application(3). To overcome these problems, we generated bispecific immune engagers using the cysteine-meditope platform. First, αCD16 was selected for NK cell engagement. The cysteine meditope tag was fused to the N- or C-terminus of an αCD16 nanobody (Figure 5A) (see online methods). Bacterially expressed N- and C-terminal meditope-αCD16 nanobodies afforded high yields of purified material and both readily reacted with the 175Cys-Fab to create HER2 and NK cell bispecific engagers. Formation of the disulfide bond was verified by non-reducing and reducing SDS-PAGE (Figure 5B).

Figure 5. Creating of bispecific NK cell engagers. A. Diagram of N- and C-terminal meditope αCD16 nanobody conjugated to the 175Cys-Fab. The Fab light and heavy chains are shown in light blue and light gray, respectively. The αCD16 domain is cyan, the the complementarity-determining regions (CDRs) are orange, and the genetically-fused meditope is green. B. SDS-PAGE (run under non-reducing conditions) showing conjugation of the 175Cys trastuzumab Fab with αCD16 containing an N- or C-terminal meditope tag. Reduction of the complexes showed they dissociate into their individual components. C. In vitro ADCC assay using bispecific conjugates shown in A, 175Cys Fab, 175Cys-IgG1 (EC50=103 pM), pertuzumab (EC50=110 pM), and trastuzumab (EC50=59 pM) (as indicated on the figure). C-terminal meditopeαCD16-175Cys-Fab (EC50=3.2 pM) potently activated ADCC, using SKBR3 cells as the target and Jurkat cells expressing FcγRIIIa as effector cells and luciferase controlled by NFAT activation. Experiments were done in triplicate. Error bars are s.d.

The efficacy of these constructs was determined using an in vitro, antibody-dependent cellular cytotoxicity assay (ADCC). The templated, C-terminal meditope-αCD16-175Cys-Fab variant demonstrated potent ADCC activity, with EC50 values of 3.2 pM and 4.7 pM (independent measurements). The ADCC activity was substantially less for the N-terminal, meditopeαCD16-Fab variant, likely reflecting steric constraints. The control individual αCD16 and 175Cys-Fab failed to elicit a response. Clinical trastuzumab, 175Cys-IgG1, and pertuzumab, a different αHer mAb, were 20- to 40-fold less potent than the C-terminal variant (Figure 5C). Moreover, the stability of the N-terminal meditope-αCD16-175Cys-Fab in


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normal rat serum was stable over 14 days at 37 °C (Figure 6A). Additionally, the templated complex remained essentially intact at glutathione concentrations up to 6.4 mM, much higher than the concentration of reduced glutathione normally present in serum (i.e., 1.02 mM) (Figure 6B)(16).

Figure 6. Stability of the N-terminal meditope-αCD16-175CysFab. A. The conjugate was incubated in rat serum for 14 days at 37°C, and stained for the kappa light chain on the Fab by western blot analysis for the kappa light chain. The disulfide bond appeared to be intact after 14 days, as no free Fab was present. B. The conjugate in either its native state (left) or SDS denatured state (right) was exposed to increasing amounts of reduced glutathione. The native state was more resistant to reduction, indicating stabilization of the disulfide bond.

Because αCD3 is commonly used to produce bispecific Tcell engagers (BiTES), we meditope-enabled three distinct αCD3-Fabs with 175Cys and reacted these Fabs with an Nterminal cysteine-meditope-modified ZHER2, an affibody that binds human HER2 with ultrahigh affinity (reported KD = 22 pM) (Figure 7A-B)(17). The sequences for human αCD3, SEQIDs 514-522, 770-778, and 1050-1234, were extracted from patent WO2014047231A1. Each templated complex showed a 5-11°C increase in overall melting temperature as compared to the individual αCD3-Fabs, establishing the broad applicability of the cysteine meditope platform for multiple unrelated Fabs (Figure S5). All three ZHER2-175Cys-Fab(αCD3) complexes activated T cells when mixed with high (SKBR3) and low (MCF7) HER2 expressing cells, whereas the Fab-only controls did not. The EC50 values for the 514-522, 770-778, and 10501234 BiTEs were 38, 54, and 34 pM, respectively, using SKBR3 cells (Figure 7C). In contrast, the EC50 values of each were 120, 180, and 140 pM, respectively, using MCF7 cells (Figure S6).

Figure 7. Creation of Bispecific T cell Enagers. A. Diagram of ZHER2 affibody fused with a meditope tag prior to reaction with the 175Cys-Fab(αCD3). As above, the Fab light and heavy chains are colored light blue and light gray, respectively. The meditope tag is shown in green and ZHER2 in blue. B. SDS-PAGE (run under non-reducing conditions) of the three 175Cys-Fabs(αCD3) bound to ZHER2 fused to an N-terminal meditope tag. C. In vitro activation of Jurkat cells expressing luciferase under the control of the NFAT pathway by the ZHER2-175Cys-Fab(αCD3) BiTEs in the presence of SKBR3 cells. Experiments were done in triplicate. Error bars are s.d.

Conjugating Small Molecules After establishing that the template-catalyzed reaction is an effective means to directly and stably conjugate biologics to mAbs and Fabs, we extended this approach to a series of therapeutically relevant small-molecules. First, PEG is frequently added to biologics to increase their serum half-life. Therefore, we attached a cysteine meditope modified with an azido group to the 175Cys-Fab and reacted the complex with 30kDa pegylated-DBCO. SDS-PAGE revealed a 30 kDa increase in mass of the Fab under non-reducing conditions (Figure S7). Second, antibodies linked to ultra-toxic compounds (antibodydrug conjugates or ADCs) are used to target specific diseased cells. We linked mertansine (DM1) or monomethyl auristatin E (MMAE), toxins used in clinically approved ADCs, to the cys-meditope and individually added these conjugates at 2.5fold excess to 175Cys-IgG1, yielding a drug-antibody ratio (DAR) of 1.84 (Figure S8, Table S4). The toxicity of each



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templated ADC to SKBR3 cells (EC50 = 110 pM for DM1175Cys and EC50 = 100 pM for MMAE-175Cys) was compared to the toxicity of the clinically approved T-DM1 (EC50 = 93 pM) (Figure S9). T-DM1, however, has an average DAR of 3.4, or ~2 fold the level of toxin compared to the DM1175Cys. Importantly, the thermal stability of the cysmeditope-based, MMAE ADC improved by 9 ºC whereas the thermal stability of MMAE ADCs using the ThiomAb approach reduced the thermal stability by 1-2 ºC(18). (Figure S10). Next, to create BiTEs using Fabs, as opposed to meditope-tagged nanobodies or other biological scaffolds, the three 175Cys-Fabs(αCD3) from above, were disulfide conjugated with TCO-cysteine meditope (to use “click”chemistry) and independently mixed with the 175CysFab(αHER2) disulfide conjugated to a tetrazine-cysteine meditope (Figure 8A). The clicked and purified products produced a band of ~100 kDa under non-reducing conditions, and bands consistent with the light and heavy chains for each Fab under reducing conditions (Figure 8B). In an in vitro assay, the clicked BiTEs simulated luciferase expression in engineered Jurkat cells mixed with SKBR3 cells. The EC50 values of the clicked BiTEs ranged from 62 to 77 pM (Figure 8C). Finally, fluorescently labeled mAbs can be used to guide surgery. Previous results have shown that fluorescence-guided surgery improves survival of tumor-bearing animals as compared to white field surgery(19, 20) . To adapt our meditope technology to this approach, we made an antibody dye conjugate (1.8 dyes per IgG) using a cysteine meditope fused to Alexa647. The dye conjugate produced specific and robust binding to antigen-bearing cells as assessed by analytical cytometry and fluorescent microscopy (Figure 9A-B), and was effectively used to image tumors in NSG mice (n=4) bearing HER2-overexpressing breast cancer tumor xenografts (Figure 9C). Immediately after whole-body imaging, the tumors and major organs were harvested and imaged. Fluorescence predominantly localized to the tumor site (Figure 9D). Similar results were observed for NSG mice bearing HER2-MCF7 tumors (Figure S11).

Figure 8. The production of BiTEs using “click” chemistry. A. Diagram of the click reaction between TCO-175Cys-Fabs(αCD3) and tetrazine-175Cys-Fab(αHER2). The Fabs were mixed at a 1:1 ratio to produce three different αCD3-αHER2 BiTEs. B. Shown is an SDS-PAGE gel (run under non-reducing conditions) of the purified BiTEs compared with the unreacted Fabs. Under strong reducing conditions, the light (LC) and heavy (HC) chains migrated at the expected mass. For space, TCO-175Cys-Fab(αCD3) and tetrazine-175Cys-Fab(αHER2) are shortened to TCO-αCD3 and tetrazine-αHER2. C. αCD3-αHER2 Fab clicked products activate Jurkat cells in the presence of SKBR3 cells. The αCD3αHER2 BiTES are able to crosslink Jurkat and SKBR3 cells to activate the NFAT pathway and produce luciferase. As expected, the Fabs alone (i.e. without the click reaction) failed to elicit a response. In the absence of SKBR3 cells no activation of NFAT was observed. Experiments were done in triplicate. Error bars are standard deviation.


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Bioconjugate Chemistry trastuzumab-meditope conjugates. D. Fluorescence images of the tumors and major organs from each mouse after the 72hr whole body image. Tumors and organs are in the same order a in d. The organs are labeled as follows: T – Tumor, K – Kidneys, S – Spleen, and L – liver.

Conclusions Taken together, these data indicate the high affinity, meditope-Fab interaction allows the efficient and stable conjugation of 175Cys-modified mAbs for multiple applications without the need for enzyme-catalyzed, post-translational modifications(21-24) or the introduction of non-natural amino acids(25)—a first, to the best of our knowledge, in the antibody field. The introduction of the meditope-binding site is straightforward and compatible with modern molecular biology approaches (e.g., synthesis of codon-optimized genes). 175Cys meditope-enabled mAbs can be made at high yield and their conjugation with functionalized meditopes is nearly stoichiometric. These features open the possibility of assembling potent biologics with agents that are otherwise cytotoxic to mammalian cells (e.g., PE38) but non-toxic in other expression systems (e.g., E. coli). Moreover, individual components mAbs and meditope conjugates can be optimized in terms of stability, affinity, etc., which is difficult to untangle when multiple domains are expressed as a single chain. Finally, the creation of these novel, functionalized cys-meditopes expands the repertoire available to this “plug-n-play” technology. Thus, the technology developed herein makes possible the rapid and efficient creation, expansion, and exploration of the therapeutic and diagnostic landscape of mAbs.

ASSOCIATED CONTENT Supporting Information. The Supporting Information is available free of charge on the ACS Publications website. Methods and supporting data: Cys_bond_BC_supplemental.docx AUTHOR INFORMATION †

Figure 9. In vitro and in vivo imaging of the meditope Alexa647 conjugate. A. FACs analysis of binding of the complex of the cysmeditope-Alexa647 conjugated to 175Cys-IgG1 to SKBR3 cells. Trastuzumab (red), 175Cys-IgG1 (orange), and 175Cys-IgG bound to the SQFDA(Ph)2CTRRLQSGGSK-Alexa647 meditope (blue) were incubated with SKBR3 cells, after which cells were stained with anti-human IgG Fc secondary antibody conjugated to Alexa488. Control untreated SKBR3 cells are shown in green. Dye-antibody ratio for 175Cys IgG was 1.8. B. Immunofluoresence images of SKBR3 cells incubated with the 175CysIgG1conjugated to the SQFDA(Ph)2CTRRLQSGGSK-Alexa647 meditope (green). C. Whole body fluorescence images of representative mice bearing BT474 HER2-overexpressing breast tumor xenografts that were injected with the 175Cys-IgGconjugated with the SQFDA(Ph)2CTRRLQSGGSK-Alexa647 meditope. Images were taken 24, 48 and 72 h after injection of the

Corresponding Author Prof. John C. Williams Email: [email protected] Phone: (626) 256-4673 Funding Sources

JCW acknowledges support from the Alicia and John Kruger Gift, WM Keck Medical Foundation, Leo and Anne Albert Charitable Trust, Carl and Roberta Deutsch Foundation, and Grant Nos. R21 CA135216 and R21 CA17608 from the NCI. We also acknowledge funding from the City of Hope Women’s Cancer Pilot Project and resources made available by the Drug Discovery and Structural Biology and Small Animal Imaging Cores, both supported by Grant No. P30 CA033572 from the NCI (PI Steve Rosen).



ACKNOWLEDGMENT We thank the current and former members of the Williams’ laboratory.

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NOTES J.C.W. and D.A.H. have multiple patents (issued and pending) covering the meditope technology, are cofounders, shareholders, and members of the SAB of Meditope Biosciences, Inc. However, all of the work reported here was funded by charitable contributions to City of Hope and federal grants (i.e., none of the research reported here was supported by Meditope Biosciences, Inc.). The remaining authors declare no competing interests.

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Template-catalyzed, disulfide conjugation of monoclonal antibodies

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